Monday, March 22, 2010

The Genome of a Microbial Eukaryote: You Can't Make This Stuff Up

New research is confirming the evolutionary conundrum of early complexity. The research shows that a microbial eukaryote, Naegleria gruberi, shares a large number of genes in common with other eukaryotes. And why is this a problem? Evolutionists have resorted to many incredible just-so stories of convergence. From intricate spider web designs to entire vision systems, evolutionists have been forced to say such designs, because they are found repeated in distant species, have evolved more than once. And while the supposed independent evolution of these striking designs is silly, even these evolutionists have not yet said that similar genes evolve independently. Until and unless they resort to such a fantasy they must say that similar genes in different species have arisen from a common ancestor. And that leads to another problem.

According to evolution, similar genes in different species have a common ancestral gene. But a great many similar genes are found in a great many different species. Consequently evolutionists are forced to conclude the common ancestor was a super ancestor. For decades now evolutionists have been jacking up the capabilities of early life. All the high-tech innovations of biology were, apparently, produced in those warm little ponds of early life.

The new research tells us that with evolution we must believe that the last common ancestor of the eukaryotes must have had at least 4133 genes. This is up from the earlier estimate of 3417, and it is a lower bound. For several reasons the number must even be significantly greater than 4133 genes if evolution is true. This continues the theme of, as one evolutionist put it, "The Incredible Expanding Ancestor of Eukaryotes."

These gene numbers alone force evolutionists to conclude that the last common ancestor of eukaryotes was already a complex organism. This is also the conclusion when the biology is compared. That early eukaryote must have had not only the vast majority of the complex DNA replication, RNA splicing and interference, and protein translation machinery, it was also capable of advanced movement and was equipped with versatile energy conversion systems.

This is truly an astonishing story evolutionists are telling us. Incredible biological capabilities, crucial to advanced life, just happened to arise rapidly in those heady days of early evolution. It was, as evolutionists now say, a giant step to an amoeba, yet a small step to man. Right. I can hear the ball bearings already.

Cornelius Hunter: These gene numbers alone force evolutionists to conclude that the last common ancestor of eukaryotes was already a complex organism.

The last common ancestor of eukaryotes was most certainly complex.

Cornelius Hunter: All the high-tech innovations of biology were, apparently, produced in those warm little ponds of early life.

Early life? When eukaryotes arrived on the scene, life had already been evolving for a billion years. Eukaryotes are as highly derived from the last common ancestor of all life as dinosaurs are from the first eukaryotes.

No. The original blog concerned the complexity of eukaryotes and argued incorrectly that this was a problem for evolutionary biology because they evolved early in the history of life. In fact, eukaryotes are highly derived, following hundreds of millions of years of evolution.

From Joe G's referenced article on echolocation.However, it is generally assumed that most of these so-called convergent traits have arisen by different genes or different mutations. Our study shows that a complex trait—echolocation—has in fact evolved by identical genetic changes in bats and dolphins.And:[O]ur findings suggest that the high-frequency acoustic sensitivities and selectivities of bat and whale echolocation appear to rely on a common molecular design of prestin.

Evolution is truly amazing. What are we to make of a theory that ostensibly relies on randomness as its core explanatory component and we see two identical designs arising in two different animals?

#John1453: An unwarranted assumption, based upon a faith in the explanatory power of the evolution world view.

Which is why you can't discuss evolution without confronting the evidence for the history of life, including Common Descent. IDers continually claim it is irrelevant, but it is always relevant, as we can see from your response.

#John1453: Life may have existed for a billion years, but there is no compelling evidence that it was evolving by way of neoDarwinian mechanisms.

Only that there is a history is relevant to the point raised. There is as much history behind the first eukaryotes as there is in front of eukaryotes.

"Notice once again that “descent with modification” does not require (or even imply) progress."

Nested hierarchies require progress.

But facts mean nothing to you and so you will blather on about "evidence" all the while never producing any positive evidence that genetic mutations- ie genetic accidents- can accumulate in such a way to do the things you are claiming they have done.

The key difference between ID and Evolutionists is that the latter try to understand and explain the problems in science with evidence (which is very widely available - try reading New Scientist regularly, with an open mind) while the former rely on their imaginary friend and insults e.g. "resorted to just so stories", "jacking up" etc - and yes I am criticising you, because you have taken a position on the basis of faith and will try any and every mechanism to undermine real science.

Joe G.:But facts mean nothing to you and so you will blather on about "evidence" all the while never producing any positive evidence that genetic mutations- ie genetic accidents- can accumulate in such a way to do the things you are claiming they have done.

Your comment is at the heart of the epistomological question I have been asking on many blogs, including this one. To repeat my question once more:

How do evolutionists know that the mechanism they propose as the explanation for the history of life can accomplish what is claimed for it?

I have never gotten a direct answer. Sure, some have pointed to common descent as the evidence for mechanism, but as you said, "Common Descent is irrelevant as to whether living organisms were designed or arose via blind, undirected (chemical) processes."

Joe G - para 2 - not sure what the specific question is as the field of evolution is vast and involves a lot of theories and facts - read Dawkins' latest - he very clearly explains how things work and cites the evidence.

I am not an expert on evolution but I am just intelligent and open minded enough to work out from a wide range of sources that evolution fits the facts better than ID and that both Christianity and Islam are laughably illogical and incoherent theologies that rely on a massive suspension of disbelief.

I am not an expert on evolution but I am just intelligent and open minded enough to work out from a wide range of sources that evolution fits the facts better than ID and that both Christianity and Islam are laughably illogical and incoherent theologies that rely on a massive suspension of disbelief.=======

Yes, but in what way? How is it that I have taken a position on the basis of faith? Since the position I take is based on science, and since evolution is based on a metaphysical faith position, I suspect rather that it is you, not I, who is operating from a basis of faith. But perhaps I have that all wrong. So please explain how it is that I have taken a position on the basis of faith, specifically.

Doublee: Evolution is truly amazing. What are we to make of a theory that ostensibly relies on randomness as its core explanatory component and we see two identical designs arising in two different animals?

As they start with very similar proteins and are selected for similar functions, it's not so surprising. It depends on the available channels leading to increased capability. Consider the simple case of convergence in the hydrodynamics of fish and dolphins.

Doublee: How do evolutionists know that the mechanism they propose as the explanation for the history of life can accomplish what is claimed for it? I have never gotten a direct answer.

Sure you have, but you haven't bothered to follow the argument through.

Doublee: Sure, some have pointed to common descent as the evidence for mechanism, ...

Common Descent can be established independently of mechanism, but sets limits on possible mechanisms.

Doublee: ... but as you said, "Common Descent is irrelevant as to whether living organisms were designed or arose via blind, undirected (chemical) processes."

As the evidence of biological evolution includes the patterns of historical descent, by saying it isn't relevant, you create a strawman of the position you reject.

CH - I must have missed something - if you are promoting ID design, I assume that you believe that there is an intelligent designer involved .... in the absence of any evidence that such a "being" exists .... other than through misrepresenting reality - having looked you up on the web, I see that I am wasting my time having a "debate" - the federal court's 2005 evaluation of the Discovery Institute says it all.

======I must have missed something - if you are promoting ID design, ======

Huh? ID was not even in the discussion.

======I assume that you believe that there is an intelligent designer involved .... in the absence of any evidence that such a "being" exists .... other than through misrepresenting reality - having looked you up on the web, I see that I am wasting my time having a "debate" - the federal court's 2005 evaluation of the Discovery Institute says it all.======

Debate? You falsely criticized me as taking "a position on the basis of faith" and trying "any and every mechanism to undermine real science." You then were unable to come up with any support for your accusations. So you know resort to some unnamed 2005 court decision. Am I in some court decision that I don't know about?

Leading atheist Richard Dawkins has called people who believe in God delusional. Yet, people who are delusional resolutely deny reality. Then the truth is that materialists, such as Richard Dawkins, are the ones who are delusional, in the purest sense of the word, since quantum mechanics has revealed, in no uncertain terms, that reality is a “consciousness centered” reality that precedes the 3 dimensional “material” reality in the first place. i.e. It is impossible for a 3 dimensional material reality to independently give rise to that which it is absolutely dependent on for its own reality in the first place. Consciousness must, of logical necessity, originally arise from the “infinite transcendent information realm” revealed by Quantum Mechanics.

So amile please explain why materialists continue to insist, after Aspect’s falsification of hidden variables, that consciousness arises from a 3-D material basis when “uncertain” 3-D material particles do not even collapse from the “quantum information waves” in the first place until a conscious observer is present. Please explain how in the world something can give rise to that which is a necessary condition for its own reality in the first place.

Why Quantum Theory Does Not Support Materialism – By Bruce L Gordon:Excerpt: Because quantum theory is thought to provide the bedrock for our scientific understanding of physical reality, it is to this theory that the materialist inevitably appeals in support of his worldview. But having fled to science in search of a safe haven for his doctrines, the materialist instead finds that quantum theory in fact dissolves and defeats his materialist understanding of the world.

Zachriel:As the evidence of biological evolution includes the patterns of historical descent, by saying it isn't relevant, you create a strawman of the position you reject.

I am not necessarily rejecting the evolution hypothesis. I am just not ready to accept it until it can be demonstrated that blind, undirected processes can be shown to be a better explanation. You and I have been down that "demonstration road" before, and I see nothing to be gained from going down that road again.

Thought Provoker, please note I said "uncertain" particle so as to point out that there really is no solid particle as many people unfamiliar with quantum mechanics believe.,,, Yet it still does not negate the theistic principle elucidated by the "quantum information wave collapse" to its "uncertain" particles being centered on a conscious observer. In fact That it would defy time space consideration at even the uncertain "particle level is actually to be expected from a theistic viewpoint. I explain my thoughts on quantum mechanics in detail in the first part of the paper here; where you may find the answers to the other questions you asked:

CH - "Turning popular opinion on its head, Hunter convincingly argues that scientists who oppose intelligent design do so for theological reasons, not empirically based arguments." but oh, someone else said that, so perhaps you just don't like evolution and do not believe in ID, but some other way we got here - in trying to find out what you believe, I found this "Here evolution aligns itself with radical skepticism. Nothing can be known to be true. If evolution is true, then not only are our minds nothing more than the product of unguided natural processes (evolutionists don't say that and you know it), but those very processes inbred a certain degree of falsehood. The evolutionist’s claim that evolution is a fact is self-refuting, for it leads to the conclusion that they cannot know that evolution is a fact." - Andrew Marvell would have been proud of you ! - the fact that you deliberately (PhD after all) misinterpreted Rivers' words is sad.

So, you falsely criticized me as taking "a position on the basis of faith" and trying "any and every mechanism to undermine real science." You then were unable to come up with any support for your accusations. And now this quote:

====="Turning popular opinion on its head, Hunter convincingly argues that scientists who oppose intelligent design do so for theological reasons, not empirically based arguments."=====

So you make the theological arguments, and I'm the one who is taking a faith position?

Zachirel"As they start with very similar proteins and are selected for similar functions, it's not so surprising. It depends on the available channels leading to increased capability. Consider the simple case of convergence in the hydrodynamics of fish and dolphins."

If you accept similar genetic mutation in species not related, you have to eliminate genetic similarities as prove of common ancestor. You cannot keep both.

Blas: If you accept similar genetic mutation in species not related, you have to eliminate genetic similarities as prove of common ancestor. You cannot keep both.

You have to look at the body of the evidence. The nested hierarchy is strongly supported across most taxa, and leads to specific empirical predictions that have been repeatedly verified. That's why a scientist can venture out into the wilderness and come back with novel organisms with a predicted range of features. Convergence often proves the rule, and Darwin discusses this all the way back in 1859.

There is no serious scientific doubt of descent with modifications. Humans and hummingbirds share a common ancestor.

Blas,if you look at a single gene in isolation, it is difficult to distinguish between convergence and common descent. however, if you look at the big picture, it becomes much easier. for example, fish and dolphins both have a torpedo shape that reduces drag in water. now, would you say that this shape is the result of convergence or because dolphins and fish share a recent common ancestor?

You might find this article interesting:http://www.ncbi.nlm.nih.gov/pubmed/19942614

It is a good example of how we can distinguish between a gene that was present in a common ancestor or the convergent evolution of a gene.

"Although the presence of SL trans-splicing in hydrozoan cnidarians, hexactinellid sponges, and ctenophores might suggest that it was present at the base of the Metazoa, the patchy distribution that is evident at higher resolution suggests that SL trans-splicing has evolved repeatedly among metazoan lineages. In agreement with this scenario, we discuss evidence that SL precursor RNAs can readily evolve from ubiquitous small nuclear RNAs that are used for conventional splicing".

The other case would be where we find that all the species in a specific lineage share the same gene, and that the sequence aligment fits in the phylogenic tree. In this case, the most likely explanation is common ancestry.

A common ancestor is the best explanation for the genes and bodies similarities in the majority of cases (at least in multicellular eucaryotes). Every new species that get it's genome fully sequenced reconfirm this (unless you are aware of specific article demonstrating this is not the case).

Once reliables trees are available (using genetic and phenotypic datas), we can then start searching for the exceptions.

Blas: The question remains, similarity in genes and bodies are prove of common ancestor or common ancestor is the most likely explanation of the similarities in some cases?

The nested hierarchy applies to morphology, genomics, embryonics and fossils in time. That there are exceptions doesn't change the fact that there is an overall pattern. The exceptions help prove the rule.

For instance, endogenous retroviruses, being virus DNA, violate the overall nested hierarchy. But they form their own nested hierarchy consistent with an insertion into the existing hierarchy. And this is consistent with the observed mechanism of retroviruses.

It would be useful if Z actually understood that statement and used it correctly. That aphorism originated at a time when "prove" meant, among other things, "test". Such a meaning is now archaic which is why many people misuse that aphorism.

Hence, the statement means "exceptions test the rule". That is, exceptions are problematic and test the adequacy of the rule to explain the extant data.

#John1453: Well, that might be true, except that it's now irrelevent as biologists have given up on constructing an accurate or realistic tree of any kind.

That is simply incorrect. Phylogenetics is a very active area of research. Entire journals, research staffs, and the lastest in information technology are involved in resolving phylogenetic trees. It is because of this intense effort that inconsistencies have been found at the root of the tree of life. The most plausible explanation is an early epoch where horizontal mechanisms were more important than vertical inheritance, and where the notion of a distinct organism may not be valid. Nevertheless, the evidence supports common descent from a single ancestral population.

#John1453: Hence, the statement means "exceptions test the rule". That is, exceptions are problematic and test the adequacy of the rule to explain the extant data.

Yes, that is the usual scientific sense. And endogenous retroviruses are an exception that tests and validates the rule.

Cornelius G. Hunter is a graduate of the University of Illinois where
he earned a Ph.D. in Biophysics and Computational Biology. He is
Adjunct Professor at Biola University and author of the award-winning Darwin’s God: Evolution and the Problem of Evil. Hunter’s other books include Darwin’s Proof, and his newest book Science’s Blind Spot
(Baker/Brazos Press). Dr. Hunter's interest in the theory of evolution
involves the historical and theological, as well as scientific, aspects
of the theory. His website is http://www.darwins-god.blogspot.com/